Multiplexed active biologic array

ABSTRACT

A method of addressing and driving an electrode array includes the step of addressing one or more electrodes within the array using a plurality of row and column lines. In one aspect of the method, a value corresponding to a voltage is stored in a local memory associated with each electrode. The addressed electrodes are then driven at the voltages corresponding to the stored values. In another aspect of the method, a driving element associated with each addressed electrode is selectively coupled with a voltage line so as to charge the electrode with the voltage on the voltage line. The device and methods may be used in the synthesis of biopolymers such as oligonucleotides and peptides.

DESCRIPTION

[0001] This Application is a continuation of U.S. application Ser. No.09/903,110, filed on Jul. 10, 2001, now pending, which is a continuationof U.S. application Ser. No. 09/364,676, filed on Jul. 30, 1999, nowissued as U.S. Pat. No. 6,258,606, which is a continuation of U.S.application Ser. No. 08/677,305, filed on Jul. 9, 1996, now issued asU.S. Pat. No. 5,965,452, all of which are incorporated by reference asif set forth fully herein.

FIELD OF THE INVENTION

[0002] The present invention relates generally to electronic systems forcarrying out and/or monitoring biologic reactions and, moreparticularly, to the design, fabrication and uses of self-addressable,self-assembling microelectronic systems for carrying out and controllingmulti-step and multiplex reactions in microscopic formats. Inparticular, these reactions include reactions such as nucleic acidhybridizations, nucleic acid amplification, sample preparation,antibody/antigen reactions, clinical diagnostics, and biopolymersynthesis, including, but not limited to, the synthesis of differentoligonucleotides or peptides at specific electrode sites.

BACKGROUND OF THE INVENTION

[0003] For some time now, substantial attention has been directed to thedesign, implementation and use of array-based electronic systems forcarrying out and/or monitoring biologic reactions.

[0004] For example, it has been recognized that electronic biosensors ofvarious types may be used to monitor (or measure) the progress ofcertain biologic reactions, and that arrays of these sensors may befabricated using techniques similar to those utilized in the integratedcircuits field. As shown in FIG. 1, a typical prior art biosensor 1 mayinclude a biospecific immobilization surface 2 having an immobilizedaffinity ligand 3 bound thereto, a transducer 4 capable of sensing theoccurrence of chemical reactions which may occur between the immobilizedligand 3 and a specific analyte, and an amplification and control unit 5for filter-ing, amplifying and translating signals generated by thetransducer 4 into various measurements useful for monitoring theprogress or occurrence of a selected biologic reaction. Biosensors ofthe type described above are discussed in some detail in ProteinImmobilization, Fundamentals & Applica-tions, R. F. Taylor, ed. (1991)(chapter 8); and Immobilized Affinity Ligand Techniques, Hermanson etal. (1992) (chapter 5).

[0005] The fabrication of an array of biosensors is disclosed, forexample, in U.S. patent application Ser. No. 07/872,582, entitled“Optical and Electrical Methods and Apparatus for Molecule Detection”(published Nov. 14, 1993 as International Publication No. WO93/22678,and hereinafter referred to as “the Hollis et al. application”). TheHollis et al. application is directed primarily to biosensory devicescomprising an array of test sites which may be electronically addressedusing a plurality of conductive leads. Various types of biosensors aredescribed for use at the test sites, and it is suggested that the testsites may be formed in a semiconductor wafer using photolithographicprocessing techniques. It is further suggested that the test sites maybe coupled to associated detection circuitry via transistor switchesusing row and column addressing techniques employed, for example, inaddressing dynamic random access memory (DRAM) or active matrix liquidcrystal display (AMLCD) devices.

[0006] In addition to the biosensor devices described above, severaldevices capable of delivering an electrical stimulus (or signal) to aselected location (or test site) within a solution or elsewhere, havebeen developed. As shown in FIG. 2, these devices often include a source6, such as a current, voltage or power source, an electrode 7 coupled tothe current source 6, a permeation layer 8 formed on one surface of theelectrode 7, and a biologic attachment layer 9 formed upon thepermeation layer 8. The permeation layer 8 provides for free transportof small counter-ions between the electrode 7 and a solution (notshown), and the attachment layer 9 provides for coupling of specificbinding entities.

[0007] Exemplary systems of the type described above are disclosed inPCT Application No. PCT/US94/12270, which was published in May 1995, andis entitled “Self-Addressable Self-Assembling Microelectronic Systemsand Devices for Molecular Biological Analysis and Diagnostics,” and PCTApplication No. PCT/US95/08570, which was published on Jan. 26, 1996,and is entitled “Self-Addressable Self-Assembling MicroelectronicSystems and Devices for Molecular Biological Application,” (hereinafter“the Heller et al. applications”) both of which are hereby incorporatedby reference. The Heller et al. applications describe electronic deviceswhich may be fabricated using microlithographic or micromachiningtechniques, and preferably include a matrix of addressablemicro-locations on a surface thereof. Further, individualmicro-locations are configured to electronically control and direct thetransport and attachment of specific binding entities (e.g., nucleicacids, anti-bodies, etc.) to itself. Thus, the disclosed devices havethe ability to actively carry out controlled multi-step and multiplexreactions in microscopic formats. Applicable reactions include, forexample, nucleic acid hybridizations, antibody/antigen reactions,clinical diagnostics, and multi-step combinational biopolymer synthesisreactions.

[0008] Additional electronic systems for interfacing with varioussolutions and/or biologic entities are disclosed in European PatentApplication No. 89-3133379.3, published Apr. 7, 1990 and entitled“Electrophoretic System;” U.S. Pat. No. 5,378,343, issued Jan. 3, 1995and entitled “Electrode Assembly Including Iridium Based MercuryUltramicroelectrode Array;” U.S. Pat. No. 5,314,495, issued May 24, 1995and entitled “Microelectronic Interface;” and U.S. Pat. No. 5,178,161,issued Jan. 12, 1993 and entitled “Microelectronic Interface.”

[0009] Those skilled in the art will appreciate, however, thatconventional electronic systems for carrying out and/or monitoringbiologic reactions (including the devices described in theabove-referenced patents and patent applications) are often bulky,expensive and, at times, difficult to control. Moreover, those skilledin the art will appreciate that, because conventional biologic systemsoften utilize “off-chip” circuitry to generate and control thecurrent/voltage signals which are applied to an array of test sites, itis often difficult without the use of special equipment to preciselycontrol the current/voltage signals generated at particular test sites.As for those conventional systems which do employ “on-chip” circuitry togenerate and control the current/voltage signals which are applied to anarray of test sites, in certain cases substantial difficulties have beenencountered where it is desired to provide separate and distinct stimulito selected electrode sites within a large array. One reason for this isthat, when single site stimulus specificity is desired withinconventional biosensor arrays, that need is often satisfied through theprovision of independent signal lines for each electrode site within thearray. As a result, conventional biologic systems are often morecumbersome and expensive than is desirable.

[0010] In view of the above-noted limitations of conventional biologicsystems, it is submitted that an improved biologic system which utilizesa minimum of “off-chip” circuitry and enables the use of large arrays ofelectrode sites while providing for very precise control of thevoltages/currents delivered at a given electrode site, would be bothuseful and desirable.

SUMMARY OF THE INVENTION

[0011] The present invention is directed to the design, implementationand use of improved electronic systems and devices for carrying outand/or monitoring biologic reactions.

[0012] In one innovative aspect, a biologic electrode array inaccordance with the present invention may comprise a matrix of electrodesites, wherein each electrode site comprises an electrode which iscoupled to a respective sample-and-hold circuit via an amplifier circuit(or driving element). The number of electrode sites can range fromseveral to at least hundreds of thousands. Each location represents atotally independent reaction site. In a preferred form, the electrodes,amplifiers and sample-and-hold circuits are integral and form an arraywithin a single semiconductor chip, such that each sample-and-holdcircuit may be loaded with a predefined voltage provided by a single,time-shared digital-to-analog converter (DAC). Further, all of thesample-and-hold circuits may be accessed through a multiplexer which maybe scanned through some or all of the electrode locations. In thisembodiment, each sample-and-hold circuit may comprise a capacitor and atransistor switching circuit, the transistor switching circuit, whenenabled, providing electrical communication between the capacitor and asource line formed in the matrix. However, in alternative embodiments,the sample-and-hold circuits may comprise some other type of memorywhich may be addressed and loaded with a signal (or value) indicative ofa characteristic of an electrical stimulus to be applied at anassociated electrode. Such alternative memories may include electricallyerasable programmable read only memory (EEPROM) cells used as an analogmemory (e.g., as in the non-volatile analog signal storage chipsproduced by Information Storage Devices, Inc., of San Jose, Calif.), orother types of circuits capable of storing control information andproducing proportional analog output values.

[0013] In another innovative aspect, a biologic electrode array inaccordance with the present invention may comprise a singlesemiconductor chip having formed thereon a memory (for example, a randomaccess memory (RAM)), a digital-to-analog converter (DAC) coupled to thememory, a counter, a row decoder coupled to the counter and to thememory, a column decoder coupled to the counter and to the memory, and amatrix of active biologic electrode sites coupled to the row decoder andthe column decoder. In use, binary values representing voltages to beapplied at the various electrode sites within the array are stored inthe memory using, for example, an external computer. Then, for eachaddress (or a selected number of addresses) within the array a binaryvalue is read out of the memory and provided to the DAC which, in turn,converts the binary value to a voltage to be stored on the “hold”capacitor at a selected address. Once all of the addresses of the array(or the selected number of addresses) have been scanned in this fashion,the process may be repeated using either the same values initiallystored in the memory or new values depending upon whether or not timevariation of the voltages/currents provided at the various electrodesites is desired. Those skilled in the art will appreciate that thescanning process should be repeated often enough such that the decayover time of the stored voltages on the sample-and-hold circuits (due tounavoidable leakage currents) does not result in an unacceptablevoltage/current errors at the electrodes. If non-volatilesample-and-hold circuits are used (i.e., if EEPROM or some equivalenttechnology is utilized), such decays may not be significant, allowingfor arbitrarily slow update rates.

[0014] In an alternative embodiment, the memory, counter and DAC may bedisposed on one or more separate chips.

[0015] In view of the foregoing, it will be appreciated that a biologicarray in accordance with the present invention provides for very precisecontrol of the potentials/currents delivered to individual electrodeswithin the array, while minimizing the utilization of “off-chip”circuitry and overall system costs. Further, by using localsample-and-hold circuits (or other local memory circuits) to control thelevel of electrical stimulus applied to particular test sites, arrays inaccordance with the present invention may achieve a level of stimulusspecificity and electrode utilization far superior to that achievedusing most prior art systems.

[0016] In another innovative aspect, the present invention provides forthe fabrication of an entire active array surface on athermally-isolated membrane containing on-board, controllable heatingelements. By cycling the temperature of the heating elements, it ispossible to perform DNA amplification in situ, for example, by thepolymerase chain reaction.

[0017] In still another innovative aspect, the present inventionprovides for the incorporation of optical fluorescence or absorptiondetection circuitry within a biologic electrode array matrix to improvecoupling of emitted photons into the detection electronics. Morespecifically, in accordance with one embodiment of the presentinvention, a biologically active electrode is formed above a suitableoptical detector such as a MOS-photodiode structure within, for example,a CMOS circuit. In such an embodiment, the electrode may be formed froma substance which is at least partially transparent, or the electrodemay be formed in such a fashion that it permits the passage of lightthrough its body to an underlying photodetector.

[0018] In yet another embodiment of the invention, a method ofaddressing and driving a biological electrode array includes the stepsof providing a chip having an array of electrodes, each electrode beingassociated with a local memory, addressing one or more electrodes withinthe array using a plurality of row and column lines, wherein eachaddressable electrode is connectable to a single row line and a singlecolumn line. The method further includes the steps of storing a value inthe local memory of each addressed electrode representative of a voltagethat is to be applied to each electrode and driving the addressedelectrodes at the voltage corresponding to the stored values.

[0019] In still another embodiment of the invention, a method ofaddressing and driving a biological electrode array includes the stepsof providing a chip having an array of electrodes, each electrode beingassociated with a driving element, addressing one or more electrodeswithin the array using a plurality of row and column lines, wherein eachaddressable electrode is connectable to a single row line and a singlecolumn line, and selectively coupling the driving element of the one ormore addressed electrodes with a voltage line so as to charge theaddressed electrode with the voltage on the voltage line.

[0020] According to another embodiment of the invention, a method ofcarrying out biological reactions on a biologic electrode array includesthe steps of providing a chip having an array of electrodes, eachelectrode being associated with a local memory. A reaction mediumincluding reactants is provided within close proximity of the array ofelectrodes. One or more electrodes within the array are addressed usinga plurality of row and column lines, wherein each addressable electrodeis connectable to a single row line and a single column line. A value isstored in the local memory of each addressed electrode representative ofa voltage that is to be applied to each addressed electrode. The one ormore addressed electrodes are then driven at the voltage correspondingto the stored values, whereby the electrical field created at the one ormore electrodes is used to react the reactants contained in the reactionmedium at a location adjacent to the electrode.

[0021] In yet another embodiment, a method of carrying out biologicalreactions on a biologic electrode array includes the step of providing achip having an array of electrodes, each electrode being associated witha driving element. A reaction medium is provided within close proximityof the array of electrodes. One or more electrodes within the array areaddressed using a plurality of row and column lines, wherein eachaddressable electrode is connectable to a single row line and a singlecolumn line. A driving element is selectively coupled to the one or moreaddressed electrodes with a voltage line so as to charge the addressedelectrode with the voltage on the voltage line, whereby the electricalfield created at the one or more electrodes is used to react thereactants contained win the reaction medium at a location adjacent tothe electrode.

[0022] In still another embodiment, a biologic electrode array comprisesa semiconductor substrate, a matrix of electrode sites disposed on thesemiconductor substrate, a local memory coupled to each electrode site,row and column decoders for addressing the electrode sites using aplurality of row and column lines, a data line for delivering to thelocal memory a value indicative of a characteristic of an electricalstimulus to be applied at the electrode site, and a driving elementlocated at each electrode site, the driving element delivering theelectrical stimulus to each electrode site in response to the storedvalue in the local memory.

[0023] In view of the foregoing, it is an object of the presentinvention to provide an improved biologic electrode array for carryingout and controlling multi-step and multiplex reactions in microscopicformats.

[0024] It is another object of the present invention to provide animproved biologic electrode array which is compact and minimizes theutilization of off-chip control circuitry, even for large numbers ofelectrodes.

[0025] It is another object of the present invention to provide animproved biologic electrode site which includes a sample-and-holdcircuit, and which may be fabricated using conventional CMOSsemiconductor fabrication techniques.

[0026] It is still another object of the present invention to provide animproved biologic electrode array which includes heating elements forenhancing the progression of reactions such as DNA amplification insitu.

[0027] It is still another object of the present invention to provide animproved biologic array which includes a plurality of optical detectorsformed beneath selected electrode sites.

[0028] It is another object of the present invention to provide a deviceand method for the combinatorial synthesis of biopolymers, such as, forexample, oligonucleotides and peptides.

BRIEF DESCRIPTION OF THE DRAWINGS

[0029]FIG. 1 is an illustration of a prior art passive biologic system.

[0030]FIG. 2 is an illustration of a prior art active biologic system.

[0031]FIG. 3 is an illustration of a biologic array in accordance withone form of the present invention.

[0032]FIG. 4(a) is an illustration of a biologic electrode site inaccordance with one form of the present invention.

[0033]FIG. 4(b) is a circuit diagram showing in more detail one of theswitching circuits and the amplifier circuit of the biologic electrodesite illustrated in FIG. 4(a).

[0034]FIG. 4(c) illustrates how those portions of the electrode siteillustrated in FIG. 4(b) might be fabricated using CMOS circuitry.

[0035]FIG. 5 is an illustration of a biologic electrode site whichincludes circuitry for monitoring an electrical characteristic of anelectrode located at the site.

[0036]FIG. 6(a) illustrates the fabrication of a combined thermallyisolated membrane and biologic electrode array, wherein the biologicelectrode array is etched onto a back side surface of a siliconsubstrate.

[0037]FIG. 6(b) illustrates the attachment of a low-thermal-conductivitychamber to the combined thermally isolated membrane and biologicelectrode array shown in FIG. 6(a).

[0038]FIG. 7 illustrates a biologic electrode site including an opticaldetector in accordance with the present invention.

[0039]FIG. 8(a) is a top view of a punctuated, partially transparentelectrode in accordance with one form of the present invention.

[0040]FIG. 8(b) is a top view of an alternative embodiment of apartially transparent electrode in accordance with the presentinvention.

DETAILED DESCRIPTION OF PREFERRED EMBODIMENTS

[0041] Turning now to the drawings, as shown in FIG. 3, a biologic array10 in accordance with one preferred form of the present invention maycomprise a matrix of active biologic electrode sites 12, a row decoder14, a column decoder 16, a counter 18, a random access memory (RAM) 20acting as a look-up table, and a digital-to-analog converter (DAC) 22.In a preferred form, each of the above listed elements may be disposedon a single semiconductor chip, and the entire array 10 may befabricated using conventional CMOS semiconductor fabrication techniques.Further, in the presently preferred form a computer (not shown) may beused to load data, as needed, into the RAM 20 via, for example, a datainput port 21.

[0042] Turning now also to FIG. 4(a), each biologic electrode site 24,which makes up the matrix of biologic electrodes 12, may comprise asample-and-hold circuit 26, an amplifier 28 and an electrode 30. In onepreferred form, the sample-and-hold circuit 26 may comprise a capacitor32 and two transistor switches 34 and 36. The switches 34 and 36 areconnected in series and, when closed, provide electrical communicationbetween a voltage source line 37 (coupled to the DAC 22) and thecapacitor 32. The switches 34 and 36 are coupled, respectively, to adesignated row select line 38 and column select line 40 formed withinthe matrix 12.

[0043] As shown in FIGS. 4(b) and 4(c), each row select line 38 and eachcolumn select line 40 may comprise, for example, a positive control line(+control line) 41 and a negative control line (−control line) 43, andeach switch 34 or 36 may comprise a CMOS transmission gate, i.e., a PMOSFET 45 having a gate region 47 coupled to the negative control line 43and a NMOS FET 49 having a gate region 51 coupled to the positivecontrol line 41. In addition, the amplifier circuit (or driving element)28 may comprise a PMOS current source 53.

[0044] In an alternative embodiment, a single switch, such as thatdescribed above, may be controlled by a two input logic gate (e.g., anAND or NAND gate) with complementary outputs (e.g., a +control line and−control line), and may be used to selectively connect the capacitor 32to the voltage source line 37. In such an embodiment, the logic gatewould respond to a coincidence of signals on the row and column selectlines 38 and 40, respectively. Further, it may be noted that in someinstances a two transistor transmission gate will not be needed, and asingle MOS transistor can be used as a switch. In such a case, the logicgate need only provide a single output to the switch.

[0045] The design, fabrication and function of counters, row decoders,column decoders, digital-to-analog converters, and random accessmemories are well known in the art and, thus, the structure andoperation of those elements are not discussed in detail herein. Rather,a general description of the function of the biologic electrode array 10is provided below.

[0046] In use, binary values representing voltages to be applied at thevarious electrode sites 24 within the matrix 12 are stored in the RAM 20(or other suitable memory device) using, for example, an externalcomputer. Then, for each address (or a selected number of addresses)within the matrix 12 a binary value is read out of the RAM 20 andprovided to the DAC 22 which, in turn, converts the binary value to avoltage to be stored on the capacitor 32 located at the selected siteaddress. An output amplifier 28 is coupled between the capacitor 32 andthe electrode 30 and provides an amplified stimulus signal to theelectrode 30. The output amplifier 28 may comprise a voltage amplifierand/or buffer and may thus amplify the voltage on the capacitor 32 andprovide an amplified voltage to the electrode 30. Alternatively, theoutput amplifier 28 may comprise a current output amplifier (forexample, a transconductance amplifier) and provide a current signal tothe electrode 30. Once all of the addresses of the matrix (or theselected number of addresses) have been scanned in this fashion, theprocess may be repeated using either the same values initially stored inthe RAM 20 or new values, depending upon whether or not time variationof the voltages/currents provided at the various electrode sites isdesired. Those skilled in the art will appreciate that the scanningprocess should be repeated often enough such that the decay over time ofthe stored voltages on the capacitors 32 (due to unavoidable leakagecurrents) does not result in an unacceptable voltage/current error atthe electrodes 30.

[0047] In equivalent and alternative forms, the counter 18, RAM 20, andDAC 22 may be placed on or off of the chip comprising theelectrophoretic electrode array, as a matter of design choice, and ifdesired, some other type of circuit (for example, a simple counter orshift register) may be used to control the sequential loading of thesample-and-hold circuits 26 located at the respective electrode sites24.

[0048] Turning now also to FIG. 5, for some applications it may bedesirable to provide for monitoring of the condition (or electricalcharacteristics) of one or more of the electrodes 30 within the matrix12. In this case, it is assumed that if the electrode is driven with aknown current, the voltage that develops is sensed, or, if the electrodeis driven with a known voltage, the current that flows is sensed. Toallow monitoring of the condition of a given electrode 30 a voltagesense amplifier 42 may be coupled to the electrode 30 and to a secondarymultiplexing bus or output pin (not shown). The voltage sense amplifier42 provides an indication of the voltage at the electrode 30 relative toan electrical ground (not shown) for the entire array or relative to aselected reference electrode (not shown) on the array. The voltage ofthe reference electrode may, in some instances, also be the ground usedfor the array. It should be noted that the output of the senseamplifiers 42 for the electrode sites 24 in the array may also bemultiplexed onto a common sense signal line, and that the signalsprovided to the common sense signal line may be de-multiplexed usingconventional circuitry, such as a sample-and-hold circuit (not shown)and an analog-to-digital converter (not shown). The common sense signalline may be separate from the common signal line (i.e., the voltagesource line 37), or it may be same line, in which case, it would be timeshared, serving for some selected periods of time to provide chargingsignals to the capacitors 32 of the electrode sites 24, and serving forother periods of time as a carrier for sense signals generated at theelectrode sites 24.

[0049] In the case where the electrodes 30 are driven by voltageamplifiers 28 and the current that flows through the electrode 30 is tobe sensed, a sense resistor (not shown) may be connected between theoutput of the voltage amplifier 28 and the electrode 30, and two inputsof a differential amplifier circuit (not shown) may be connected acrossthe sense resistor. In such an embodiment, the signal generated at theoutput of the differential amplifier will be proportional to the currentflowing through the electrode 30.

[0050] As explained to some extent above, while the embodimentsillustrated in FIGS. 4(a) and 5 employ two switches 34 and 36 connectedin series to control the loading of the capacitor 32 (one switch beingcontrolled by each of the row and column lines, respectively) thoseskilled in the art will appreciate that the switching function may beimplemented in any of a number of ways. For example, it would beconsidered equivalent to replace the switches 34 and 36, shown in FIGS.4(a) and 5, with CMOS transmission gates or a combination of an AND gateand a switch.

[0051] Turning again to FIG. 4(c), in a preferred form the biologicarray 10 may be fabricated using a CMOS or other active circuit process.Moreover, those skilled in the art will appreciate that completelyfabricated CMOS circuitry embodying some or all of the above-describedfunctions may be post-processed to form the complete active biologicelectrode array 10 described above. For example, as illustrated in FIG.6, the biologic electrodes 30 may be disposed atop the underlying CMOScircuitry and then protected with an overlapping passivation layer 44.Further, openings in the passivation layer 44 may be fabricated toexpose the active regions of the biologic electrodes 30 as well as anyrequired peripheral interconnection sites, e.g., bond-pads (not shown).In such an embodiment, the electrodes 30 may be fabricated fromelectrochemically suitable materials, such as gold, iridium or platinum,and may be deposited and patterned using conventional thin-filmdeposition techniques. The passivation layer 44 may comprise, forexample, plasma-deposited silicon nitride and/or silicon carbide, andopenings in the passivation layer 44 may be formed using conventionalmicrofabrication techniques such as plasma etching. Finally, ifbiomolecules are to be bound on or near the surface of the electrodes30, coupling agents and/or intermediate layers (shown in FIG. 7) may beused.

[0052] Turning now to FIGS. 6(a) and 6(b), in another preferred form theentire active surface of the biologic array 10 may be formed on athermally-isolated membrane 46 containing one or more on-board,controllable heating elements (not shown). The thermally-isolatedmembrane can be formed using micromachining techniques well-known in theart. For example, the back-side of the completed CMOS waver containingthe biologic array circuitry and electrodes can be coated with asuitable etch mask (e.g., silicon nitride). The silicon nitride ispatterned using standard techniques to form openings where the membraneis to be formed. The membranes are formed by submerging the wafer in anetching solution (e.g., tetramethylammononium hydroxide loaded withdissolved silicon, as described in Klassen, et al., “MicromachinedThermally Isolated Circuits,” Proceedings of the Solid-State Sensor andActuator Workshop, Hilton Head, S.C., Jun. 3-6, 1996, pp. 127-131). Themembrane can thus be temperature cycled to allow DNA amplification insitu. Further, controllable heating of the membrane may be accomplishedthrough the use of an array of resistors or appropriately biased MOSFETS(metal oxide semiconductor field effect transistors) distributedthroughout the membrane area. Thus, if a solution 48 (shown in FIG.6(b)) overlying the array 10 is provided with DNA and suitable chemicalsto carry out a polymerase chain reaction (PCR) to amplify the DNA,cycling the temperature of the membrane will allow the desiredamplification. If thermal feedback is desired, the temperature of themembrane may be readily determined. For example, the temperaturecoefficient of resistance of the heater resistors or the forward voltageof diodes incorporated into the membrane may be utilized to provide anindication of the solution temperature. Finally, once the DNA containedwithin the solution 48 is amplified, appropriate chemicals may beinjected into the chamber 50 to effect one or more desired analysissteps. Examples of such chemicals are restriction enzymes, fluorescentlabels and intercalcators, etc.

[0053] An exemplary micromachined, membrane-based DNA amplificationsystem has been demonstrated by Northrup, et al. (see Northrup et al.,“DNA Amplification with a Microfabricated Reaction Chamber,” Proceedingsof Transducers '93, the 7th International Conference on Solid StateSensors and Actuators, Yokohama, Japan, Jun. 7-10, 1993, pp. 924-926,which is incorporated herein by reference) and, thus, the specificstructure and operation of the membrane-based DNA amplification systemis not discussed herein in detail. However, it should be noted that theNorthrup et al. system provides merely for thermal cycling, and has noanalysis or biologic electrode control capabilities. Thus, it isbelieved that those skilled in the art will find a biologic array inaccordance with present invention to be highly advantageous, as such anarray allows for in situ DNA amplification and subsequent analysis usinga single device.

[0054] Turning now to FIG. 7, for some applications, it may be desirableto incorporate optical fluorescence or transmittance detection circuitrydirectly into the electrode matrix 12 to improve coupling of emitted ortransmitted photons into any provided detection electronics. In the caseof fluorescence detection, the entire array would be illuminated withlight at wavelength(s) known to excite fluorescence in the fluorescentlylabeled biomolecules such as DNA or intercalators between DNA strands.This light would be detected by the optical detection means located ateach site. In the case of transmittance detection, the entire arraywould be illuminated with light at wavelength(s) known to be attenuatedby the presence of the biomolecules of interest (i.e., the light atthose wavelengths is absorbed by the biomolecules) the presence of thebiomolecules of interest at a given electrode site would be detected byan attenuation of the light sensed by the optical detector local to thatsite. This approach can greatly improve the signal-to-noise ratio (SNR)over the use of an imaging camera remote to the biologic-array 10. Inessence, this involves combining a biologically active electrode (withor without active multiplexing circuitry) above a suitable opticaldetector 50 such as a MOS-photodiode or a charge-coupled device (CCD)structure. In such an embodiment, it may be desirable to utilizetransparent electrodes, such as those formed from indium tin oxide(ITO), or it may be desirable to utilize a slitted or punctuatedelectrode structure, such as that shown in FIGS. 8(a) and 8(b). Byproviding orifices 54 (as shown in FIG. 8(a)) or troughs 56 (shown inFIG. 8(b)) through the surface of the electrode 52 it is possible toallow the passage of light through the electrode 52 to the opticaldetector 50. Those skilled in the art will appreciate that byeliminating the need for an external camera and retaining the ability toperform biologically-controlled hybridizations (or other molecularinteractions), the overall cost of a complete analysis system can begreatly reduced.

[0055] With respect to combinatorial synthesis, the device allows verylarge numbers of sequences to be synthesized on the array. The basicconcept for combinatorial synthesis involves the use of free fieldelectrophoretic transport to deliver, concentrate, and react monomers,coupling reagents, or deblocking reagents at specific addressableelectrode sites on the device. The concept capitalizes on the inherentability of the device to electronically protect other electrode sites onthe device.

[0056] While the invention of the subject application may take severalalternative and equivalent forms, specific examples thereof have beenshown in the drawings and are herein described in detail. It should beunderstood, however, that the invention is not to be limited to theparticular forms or methods disclosed, but to the contrary, theinvention is to cover all modifications, equivalents, and alternativesfalling within the spirit and scope of the appended claims.

What is claimed is:
 1. A method of addressing and driving a biologicelectrode array comprising the steps of: providing a chip having anarray of electrodes, each electrode being associated with a localmemory; addressing one or more electrodes within the array using aplurality of row and column lines, wherein each addressable electrode isconnectable to a single row line and a single column line; storing avalue in the local memory of each addressed electrode representative ofa voltage that is to be applied to each addressed electrode; and drivingthe addressed electrodes at the voltage corresponding to the storedvalues.
 2. The method of claim 1 wherein the local memory stores abinary value representing a voltage to be applied to the addressedelectrode.
 3. The method of claim 1 wherein the addressing step isperformed using a row decoder and a column decoder.
 4. The method ofclaim 1 wherein the local memory is an EEPROM.
 5. A method of addressingand driving a biologic electrode array comprising the steps of:providing a chip having an array of electrodes, each electrode beingassociated with a driving element; addressing one or more electrodeswithin the array using a plurality of row and column lines, wherein eachaddressable electrode is connectable to a single row line and a singlecolumn line; selectively coupling the driving element of the one or moreaddressed electrodes with a voltage line so as to charge the addressedelectrode with the voltage on the voltage line.
 6. The method of claim 5wherein the voltage applied to the voltage line is changed betweendifferent voltages.
 7. A method of carrying out biological reactions ona biologic electrode array comprising the steps of: providing a chiphaving an array of electrodes, each electrode being associated with alocal memory; providing a reaction medium including reactants withinclose proximity of the array of electrodes; addressing one or moreelectrodes within the array using a plurality of row and column lines,wherein each addressable electrode is connectable to a single row lineand a single column line; storing a value in the local memory of eachaddressed electrode representative of a voltage that is to be applied toeach addressed electrode; and driving the one or more addressedelectrodes at the voltage corresponding to the stored values, wherebythe electrical field created at the one or more electrodes is used toreact the reactants contained in the reaction medium at a locationadjacent to the electrode.
 8. The method according to claim 7 whereinthe reactants are nucleic acids.
 9. The method according to claim 8wherein the reaction synthesizes oligonucleotides.
 10. The methodaccording to claim 7 wherein the reactants are amino acids.
 11. Themethod according to claim 10 wherein the reaction synthesizes peptides.12. The method according to claim 9 wherein an array of oligonucleotidesis synthesized proximal to a surface of the chip containing the array ofelectrodes.
 13. The method according to claim 7 wherein the reactioncomprises deprotecting a reactant disposed proximal to the chargedelectrode.
 14. The method according to claim 7 wherein the one or moreelectrodes are positively charged so as to hydrolyze water.
 15. A methodof carrying out biological reactions on a biologic electrode arraycomprising the steps of: providing a chip having an array of electrodes,each electrode being associated with a driving element; providing areaction medium including reactants within close proximity of the arrayof electrodes; addressing one or more electrodes within the array usinga plurality of row and column lines, wherein each addressable electrodeis connectable to a single row line and a single column line; andselectively coupling the driving element of the one or more addressedelectrodes with a voltage line so as to charge the addressed electrodewith the voltage on the voltage line, whereby the electrical fieldcreated at the one or more electrodes is used to react the reactantscontained in the reaction medium at a location adjacent to theelectrode.
 16. The method according to claim 15 wherein the reactantsare nucleic acids.
 17. The method according to claim 16 wherein thebiological reaction synthesizes oligonucleotides.
 18. The methodaccording to claim 15 wherein the reactants are amino acids.
 19. Themethod according to claim 18 wherein the reaction synthesizes peptides.20. The method according to claim 17 wherein an array ofoligonucleotides is synthesized proximal to a surface of the chipcontaining the array of electrodes.
 21. The method according to claim 15wherein the biological reaction comprises deprotecting a reactantdisposed proximal to the charged electrode.
 22. The method according toclaim 15 wherein the one or more electrodes are positively charged so asto hydrolyze water.
 23. An biologic electrode array comprising: asemiconductor substrate; a matrix of electrode sites disposed on thesemiconductor substrate; a local memory coupled to each electrode site;row and column decoders for addressing the electrode sites using aplurality of row and column lines; a data line for delivering to thelocal memory a value indicative of a characteristic of an electricalstimulus to be applied at the electrode site; and a driving elementlocated at each electrode site, the driving element delivering theelectrical stimulus to each electrode site in response to the storedvalue in the local memory.
 24. The device of claim 23 wherein theelectrical stimulus is a voltage.
 25. The device of claim 23 wherein therow and column decoders are disposed on the semiconductor substrate. 26.The device of claim 23 wherein at least a portion of the array is formedusing CMOS fabrication techniques.
 27. The device of claim 23 furthercomprising a permeation layer disposed over the matrix of electrodesites.
 28. The device of claim 23 wherein the data line delivers abinary value to the local memory.